Each base has its own quality value. Assembly will allow only
values between 1 and 99 inclusive. A quality value of 0 means that this base
should be ignored. A quality value of 100 means that this base is definitely
correct and the consensus will be forced to be the same base type and will be
given a consensus confidence of 100. If two conflicting bases both have a
quality of 100 the consensus will be a dash with a confidence of 0.

Newly added bases or replaced bases are assigned their own quality values. By
default these are both 100. The "Set Default Confidence" option in the
settings menu allows these values to be changed.

Several keyboard commands are available to edit the quality value of an
individual base. The '[' and ']' keys set the quality to 0 and 100
repsectively. To increment or decrement the confidence of a base by 1 use
Shift plus the Up and Down arrow keys. To increment or decrement by 10 use
Control plus the Up and Down arrow keys. The editor will beep if you reach
quality 0 or 100. Finally note that quality values can also be made visible by
the use of grey scales for the sequence background colour. See section Show Reading and Consensus Quality.

The cutoff data is displayed by pressing the "Cutoffs"
toggle at the top of the editor. The cutoff sequence will be
displayed in grey. We call the boundary between the cutoff data and
the used data the cutoff position. These positions can be shifted
left or right for each end of the reading using the Meta Left-arrow
and Meta Right-arrow keys respectively. As keyboards may not have a
meta key, Control Left-arrow and Control Right-arrow also have the
same effect. These key combinations adjust the cutoff positions by a
single base at a time. They only work when the cursor is on the very
first or very last "used" base, depending on which cutoff you wish
to adjust.

If large changes are required the cutoffs can be "zapped" to
new positions using the "<" and ">" keys. To use these, place the
editing cursor to the position required (which may be within the
cutoff data or the used data) and press the "<" key to set the left
cutoff to the base between the cursor and the base leftwards of the
cursor. Similarly ">" sets the right cutoff to the base between the
cursor and the base leftwards of the cursor. Note that many
keyboards have "<" and ">" above the "," and "." keys. In this case
you will need to press Shift in conjunction with "," and "." to
perform the operations.

This page is maintained by
staden-package.
Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_unix_53.html